Contacts of the helix formed by residues 218 - 235 (chain C) in PDB entry 4KZZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 218 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 5.4 2.5 - - + +
93C LYS* 1.8 72.5 - - + +
95C MET* 5.1 4.7 - - + -
112C PHE* 4.0 27.6 - - + -
194C VAL* 5.5 14.3 - - + +
215C THR 4.1 5.6 + - - -
216C ALA 2.9 11.8 + - - +
217C THR* 1.3 68.9 - - - +
219C GLY* 1.3 90.7 + - - +
220C ASN 3.1 0.9 - - - -
221C PHE* 3.8 9.6 - - + +
222C ALA* 3.0 27.1 + - + +
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Residues in contact with GLY 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 3.9 20.8 - - - -
124C LEU* 5.9 0.9 - - - +
126C MET* 5.1 0.6 - - - +
217C THR 2.3 18.4 + - - -
218C LEU* 1.3 86.9 - - - +
220C ASN* 1.3 55.4 + - - -
222C ALA* 4.3 3.5 - - - +
223C LYS* 3.2 36.2 + - - +
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Residues in contact with ASN 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C CYS* 2.6 52.9 + - - +
174C GLY* 3.0 21.7 + - - -
175C SER* 4.5 0.2 + - - -
176C VAL* 3.7 17.5 - - + +
217C THR* 3.2 17.9 + - - +
219C GLY* 1.3 76.6 - - - +
221C PHE* 1.3 58.5 + - - +
223C LYS* 3.4 2.3 + - - +
224C ALA* 3.0 26.0 + - - +
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Residues in contact with PHE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C VAL* 3.7 20.3 - - + +
178C VAL* 3.7 20.0 - - + +
192C ALA* 4.4 6.3 - - + -
194C VAL* 3.7 16.4 - - + -
195C PRO* 2.4 70.2 - - + -
211C ALA* 5.0 11.9 - - + -
215C THR* 3.8 28.0 - - - +
217C THR 4.8 0.2 - - - -
218C LEU* 3.2 13.6 + - - +
220C ASN* 1.3 75.5 - - - +
222C ALA* 1.3 73.7 + - + +
224C ALA 3.5 0.5 + - - -
225C THR* 3.1 22.2 + - + -
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 4.6 14.1 - - + -
112C PHE* 6.4 1.8 - - + -
124C LEU* 4.5 21.3 - - + -
194C VAL* 4.6 6.1 - - + -
198C LEU* 3.7 5.0 - - + +
218C LEU* 3.0 14.1 + - + +
219C GLY* 4.3 3.8 - - - +
221C PHE* 1.3 89.2 - - + +
223C LYS* 1.3 59.2 + - - +
225C THR* 2.7 28.5 - - + +
226C PHE* 2.8 13.2 + - - +
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Residues in contact with LYS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 4.8 10.3 - - + +
126C MET* 2.6 45.9 - - + +
173C CYS* 3.7 24.7 - - - -
219C GLY 3.2 21.4 + - - +
220C ASN* 3.5 6.7 - - - +
221C PHE 3.2 0.4 - - - -
222C ALA* 1.3 77.9 - - - +
224C ALA* 1.3 54.9 + - - +
226C PHE* 3.3 8.9 + - + +
227C ASP* 2.7 39.4 + - - +
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Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C GLY* 3.2 32.1 - - - +
173C CYS* 3.8 6.0 - - - +
176C VAL* 3.8 17.5 - - + +
178C VAL* 4.0 10.3 - - + -
220C ASN 3.0 16.7 + - - +
221C PHE 3.9 4.9 - - - +
222C ALA 3.3 0.2 - - - -
223C LYS* 1.3 72.3 - - - +
225C THR* 1.3 55.6 + - - +
227C ASP* 3.1 11.5 + - - +
228C ALA* 2.7 29.6 + - - +
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Residues in contact with THR 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C VAL* 3.8 20.6 - - - +
180C LEU* 4.4 4.7 - - - +
195C PRO* 4.8 10.8 - - + +
198C LEU* 3.2 25.6 - - + -
199C LEU* 4.2 19.4 - - - +
221C PHE* 3.1 12.7 + - + -
222C ALA* 2.7 33.2 - - - +
224C ALA* 1.3 79.5 - - - +
226C PHE* 1.3 57.1 + - - +
228C ALA* 3.1 7.4 + - - +
229C ILE* 3.0 31.1 + - - +
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Residues in contact with PHE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C VAL* 3.7 21.5 - - + -
123C GLY* 2.7 50.5 - - - -
124C LEU* 3.2 26.0 - - + -
146C SER* 4.0 15.7 - - - -
148C VAL* 4.2 9.0 - - + -
198C LEU* 3.2 22.2 - - + -
222C ALA 2.8 17.1 + - - +
223C LYS* 3.3 11.9 - - + +
224C ALA 3.1 0.2 - - - -
225C THR* 1.3 75.1 - - - +
227C ASP* 1.3 61.6 + - - +
229C ILE* 2.8 31.0 - - + +
230C SER* 2.9 15.5 + - - -
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Residues in contact with ASP 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C GLY* 4.1 12.1 - - - -
172C ARG 4.0 11.8 - - - +
173C CYS* 4.6 3.3 - - - +
223C LYS* 2.7 28.7 + - - +
224C ALA* 3.1 10.4 + - - +
226C PHE* 1.3 75.9 - - - +
228C ALA* 1.3 65.5 + - - +
230C SER* 3.3 6.6 + - - -
231C LYS* 3.1 31.6 + - + +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C VAL* 2.3 45.3 - - + +
170C THR 4.0 2.5 - - - -
171C GLY* 3.7 19.5 - - - +
178C VAL 4.0 7.2 - - - +
180C LEU* 4.1 11.4 - - + -
224C ALA 2.7 14.6 + - - +
225C THR* 3.1 13.8 + - - +
227C ASP* 1.3 75.8 - - - +
229C ILE* 1.3 59.6 + - - +
231C LYS* 3.0 9.4 + - - +
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C VAL* 3.2 35.0 - - + -
148C VAL* 3.9 7.6 - - + -
149C PRO 4.4 2.6 - - - +
150C VAL* 4.3 14.6 - - + +
180C LEU* 3.7 12.8 - - + -
198C LEU* 4.0 5.6 - - + -
199C LEU* 3.5 31.9 - - + -
202C ALA* 4.9 3.6 - - + -
204C ILE* 5.8 2.2 - - + -
225C THR* 3.0 11.8 + - - +
226C PHE* 2.8 35.7 - - + +
228C ALA* 1.3 75.5 - - - +
230C SER* 1.3 77.0 + - - +
231C LYS 3.1 0.9 + - - -
232C THR* 3.0 29.3 + - - +
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Residues in contact with SER 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C VAL* 3.2 33.9 - - - +
149C PRO* 4.4 15.7 - - - +
226C PHE* 2.9 21.8 + - - -
227C ASP* 3.7 6.7 - - - -
228C ALA 3.2 0.2 - - - -
229C ILE* 1.3 81.4 - - - +
231C LYS* 1.3 61.0 + - - +
232C THR 3.2 0.9 + - - -
233C TYR* 3.5 15.4 + - - +
234C SER* 4.2 4.3 + - - -
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C VAL* 4.0 10.2 - - + +
170C THR* 2.9 47.3 + - - +
171C GLY* 4.7 2.2 - - - -
227C ASP* 3.1 23.9 + - + +
228C ALA 3.0 10.8 + - - +
230C SER* 1.3 77.2 - - - +
232C THR* 1.3 63.2 + - - +
233C TYR 3.2 0.4 - - - -
234C SER* 3.0 25.1 + - - +
235C TYR* 3.1 23.5 + - - +
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Residues in contact with THR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C VAL* 3.8 2.7 - - + -
151C ARG* 2.8 55.2 + - - +
165C VAL* 3.9 14.8 - - + -
166C ARG* 6.2 1.7 - - - +
169C VAL* 3.6 29.2 - - + -
180C LEU* 5.6 1.6 - - + -
229C ILE* 3.0 22.9 + - - +
231C LYS* 1.3 77.8 - - - +
233C TYR* 1.3 64.0 + - - +
235C TYR* 3.2 20.6 + - - +
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLU* 5.7 1.2 + - - -
149C PRO* 2.8 51.1 - - + +
150C VAL 2.9 33.8 + - - -
151C ARG* 3.6 28.4 + - - +
230C SER 3.5 5.1 + - - +
231C LYS 3.2 1.0 - - - -
232C THR* 1.3 81.8 + - - +
234C SER* 1.3 61.2 + - - +
235C TYR 3.5 6.9 + - - +
240C LEU* 4.9 5.9 - - - +
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Residues in contact with SER 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C SER 4.4 2.6 + - - -
231C LYS* 3.0 22.0 + - - +
233C TYR* 1.3 76.5 - - - +
235C TYR* 1.3 63.7 + - - +
236C LEU* 3.4 4.3 + - - +
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Residues in contact with TYR 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ARG* 4.3 3.3 + - - -
166C ARG* 6.2 1.8 - - + -
167C CYS* 3.3 36.8 - - + -
168C LYS* 3.4 31.1 + - - +
169C VAL* 4.1 20.4 - - + -
231C LYS* 3.1 19.0 + - - +
232C THR* 3.2 15.1 + - - +
233C TYR 3.6 8.5 - - - +
234C SER* 1.3 78.4 - - - +
236C LEU* 1.3 71.8 + - - +
237C THR* 3.9 10.1 + - + -
240C LEU* 3.6 13.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il